Git hands-on session with command line

Working on your own

Create a repo

1. Go to GitHub and login
2. Follow this tutorial to create a repo

Clone a repo to work locally

1. Install git
2. Configure git
3. Follow this tutorial to clone your repo

Tip: adapt git configuration to use your favourite editor

git config --global core.editor gedit

Make a commit

1. Open your favourite text editor
2. Update the README.md
3. Commit your changes

Make a commit

1. Check the differences: git status and git diff
2. Commit your changes with git commit:

   • Write commit message in editor:

     git commit README.md

   • Write commit message inline:

     git commit -m 'Proper commit message README.md'

Push your changes to backup your work

• Command git push:

  git push origin master

Go to your repo on GitHub to verify

Create logical commits

1. Make 2 unrelated changes to your README.md locally
2. Create one commit for each change.
3. Do not push (yet)

Create logical commits

git add -p README.md

Create a conflict

Update your README.md on GitHub,
on a line you also edited locally

Conflict!

git pull origin master

Keep calm and resolve conflict

1. Open README.md in text editor:

   <<<<<<< HEAD
   A simple analysis to visualize my favourite fruit colour.
   =======
   A simple analysis to discover my favourite fruit color.
   >>>>>>> origin/master

2. Choose what you want to keep:

   A simple analysis to discover my favourite fruit colour.

3. Commit and push

   git add <fixed files>
   git commit
   git push origin master

Resolve conflict

Add a file

1. Add a fruits.csv file in a /data directory
2. Link to this file in the README.md

Add a file

git commit -am "My message"
takes all changes in a single commit

git add data/fruits.csv
git commit -am "Add data file"
git push origin master

Undo or adapt last commit: command line

git revert HEAD

Tip: git revert can be applied for more functionality.
See this tutorial for more in depth information on undoing commits.

Tip: git reset HEAD~ will unstage changes
(similar to Github Desktop)

View history

1. git log
2. Copy a HASH
3. git checkout HASH
4. Check the local directory and files on your computer
5. git checkout master

Create a branch to experiment

1. Create a branch
2. Add an analysis file in a /src directory
3. Commit
4. Switch between branches

Create a branch to experiment: command line

1. Create a branch by a checkout to new branch, git checkout -b:

   git checkout -b analysis-script

2. Get an overview of your branches: git branch
3. git add a file to the repository

4. Go back to the status of the master:

   git checkout master

5. Verify your local directory structure: where are your files?

6. Go back to the status of the new branch:

   git checkout analysis-script

Create a pull request to include your work

git push origin analysis-script

Review your pull request

Review your pull request

1. Review
2. If OK, merge pull request
3. Delete branch

Update local master after remote merge

git fetch origin
git checkout master
git merge --ff-only origin/master
git branch -d analysis-script

Cfr. local merge: git checkout master and git merge analysis-script

Exclude files

• in any programming language, some files are derivatives
• sensitive information (passwords,…)
• a folder with large data files that should not be in the history (and backuped elsewhere!)
• a temp/ folder for just garbage you create/…

.gitignore to the rescue!

Exclude files: command line

1. Go to master branch git checkout master
2. Create a new file password.txt with the words SECRET
3. git status and git diff
4. Create a file .gitignore to exclude the password.txt file
5. git status and git diff
6. git commit your adaptation to the .gitignore file
7. git push your changes to GitHub
8. Verify the .gitignore file on GitHub

Working together

Teaming up

• Team up with two or three persons
• Let one person invite the others, provide them with read/write access as explained in this tutorial

Invite collaborators

Invite collaborators

Collaboration: issues

• Raise an issue online
• Provide issues with an appropriate label
• Assign your colleague to the issue

Collaboration: online adaptations

• Make an adaptation to an online file
• Propose a pull request and assign your collaborator
• Merge the adaptation to the master branch

Collaboration: local adaptations

Working local - merging online

• As collaborator, clone the other repository to your local computer
• Create a new branch with a different name
• Adapt the content of a file
• commit your adaptation
• push your branch to the remote repository
• Go to GitHub and make a pull request
• Revise the work and merge online when appropriate
• Update your local work
• Check if all adaptations are represented in your local files

Tip: All functionalities are available in the previous sections

Release

Once you are satisfied with the status of your analysis, it makes sense to create a release:

• For publications (DOI)
• For code/software development versions
• For course notes

Follow this tutorial to create a release.

Alias usage for command line

As an example, give it your flavour:

alias gcl='git clone'

alias gs='git status'
alias gd='git diff --word-diff'

alias ga='git add'
alias gap='git add -p'
alias gcm='git commit -v -m'
alias gcam='git commit -am'

alias gch='git checkout'
alias gchb='git checkout -b'

alias gfo='git fetch origin'

alias gm='git merge'
alias gpl='git pull'
alias gps='git push'
alias gplom='git pull origin master'
alias gpsom='git push origin master'
alias gplfm='git fetch origin; git checkout master; git merge --ff-only origin/master'

alias glog="git log --graph --pretty=format:'%C(bold)%h%Creset%C(magenta)%d%Creset %s %C(yellow)<%an> %C(cyan)(%cr)%Creset' --abbrev-commit --date=relative"

Some more advice:

• Commit often, make small commits
• Don’t mix changes in 1 commit
• Think about your commit messages
• Keep your code clean, avoid huge one-liners
• Use branches (!)
• Don’t keep long-lived branches (form of technical debt)

There’s no such thing, as a free lunch…

Information combined at INBO Tutorials website.
You’re welcome to provide issues, pull requests,…